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<h1 class="title toc-ignore">Advanced tutorial</h1>



<div id="introduction" class="section level1">
<h1>Introduction</h1>
<p>Harmony uses a set of parameters to ensure the different components
of the algorithm work in harmony! By default, several of these
parameters are set by the algorithm using heuristics or empirical
values. Most of the time, the end-user does not need to find optimal
values to run Harmony. In this vignette, we will be going through some
use cases where user need to intervene and optimize the data or
parameters harmony.</p>
<p>There are two reasons that someone a user may need to change the
parameters. The first one is to increase the quality of the data
integration. The second one is to improve the performance of
harmony.</p>
</div>
<div id="harmony-algorithm-objective-diverges-after-a-number-of-correction-steps" class="section level1">
<h1>Harmony algorithm objective diverges after a number of correction
steps</h1>
<p>For some datasets, the objective function may diverge after a few
steps. Here we are going to be looking into the Jurkat dataset that is
bundled with harmony.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">library</span>(harmony)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="co">#&gt; Loading required package: Rcpp</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="fu">library</span>(ggplot2)</span></code></pre></div>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a></span>
<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="do">## Old</span></span>
<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a></span>
<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb2-5"><a href="#cb2-5" tabindex="-1"></a><span class="do">## HarmonyMatrix(bos, opt.args = list(lambda = c(0,1)))</span></span></code></pre></div>
</div>
<div id="an-example-of-a-problematic-dataset" class="section level1">
<h1>An example of a problematic dataset</h1>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="do">## Source required data</span></span>
<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="do">## data(&quot;celllines&quot;)</span></span>
<span id="cb3-3"><a href="#cb3-3" tabindex="-1"></a></span>
<span id="cb3-4"><a href="#cb3-4" tabindex="-1"></a><span class="do">## cell_lines &lt;- zeros()</span></span>
<span id="cb3-5"><a href="#cb3-5" tabindex="-1"></a><span class="do">## pbmc &lt;- CreateSeuratObject(counts = , project = &quot;jurkat&quot;, min.cells = 5)</span></span>
<span id="cb3-6"><a href="#cb3-6" tabindex="-1"></a></span>
<span id="cb3-7"><a href="#cb3-7" tabindex="-1"></a><span class="do">## Separate conditions</span></span>
<span id="cb3-8"><a href="#cb3-8" tabindex="-1"></a></span>
<span id="cb3-9"><a href="#cb3-9" tabindex="-1"></a><span class="do">## pbmc@meta.data$stim &lt;- c(rep(&quot;STIM&quot;, ncol(stim.sparse)), rep(&quot;CTRL&quot;, ncol(ctrl.sparse)))</span></span></code></pre></div>
<div id="input-data" class="section level2">
<h2>Input data</h2>
</div>
<div id="number-of-pcs" class="section level2">
<h2>Number of PCs</h2>
<p>Using the correct number of components can become very important in
certain scenarios.</p>
</div>
<div id="nested-data" class="section level2">
<h2>Nested data</h2>
</div>
</div>
<div id="harmony-algorithm-parameters" class="section level1">
<h1>Harmony Algorithm parameters</h1>
<div id="theta" class="section level2">
<h2>theta</h2>
</div>
<div id="lambda" class="section level2">
<h2>lambda</h2>
</div>
<div id="sigma" class="section level2">
<h2>sigma</h2>
</div>
<div id="nclust" class="section level2">
<h2>nclust</h2>
</div>
</div>
<div id="controlling-harmony-flow" class="section level1">
<h1>Controlling harmony flow</h1>
<div id="section" class="section level2">
<h2></h2>
</div>
<div id="section-1" class="section level2">
<h2></h2>
</div>
</div>



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